I honestly don't cry much, so the only anime I have that made me shed tears are these two:
Steins;Gate (Episode 22, Kurisu moments all the way, which left me screaming at my computer the first 5 min of ep 23)
Angel Beats (I cried like a baby, and I feel no shame in this, its still fresh to since a friend convinced me to watch it about a week ago... just after Christmas.. I marathoned it all in one night... I still need to kill him for ruining my happy holiday spirit).

I cried my ass off in clannad after storys like 5 times or more,and i cried seeing gundam seed and destiny,and fate stay night during the end.also teared of sheer epicness that is gundam 00 and the movie.angel beats ending i got owned i ciried like a baby.code geass and more i cant remember for now.

I don't really have water leak from my eyes unless something flew in it. But I found these to be tough to handle w/o a few secs of waterworks.

Tokyo Magnitude 8.0 I wept so many manly tears. A real heart breaker that was.
Elfen Lied. That one was so sad, it was hard not to find a place to not weep.
Gurren Lagann. That was tough to take but I only shed a few tears. Messed up how things went in that anime but it was good.

i'm a sucka at sheding my man tears, a good story hits me where it hurts, Not gonna get into ones like Clanned or Ef because those are obvious tear jerkers and good but top ones would prolly be, not in any order..

Eflien Lied (when the backstory's revealed)
Sankarea (whole cituations sad as fuck)
Kara no Kyoukai (cant remeber exact moments but tons of em)
Tasogare_Otome_x_Amnesia (towards the end it reved up the story)
Ano Hana (fucking sad as all hell all over)
Usagi Drop (didnt even think i'd like the show and it ended up being amazing and heartwarming)
Mirai Nikki (alot of parts)
Tokyo Magnitude

Spoiler Alert! Click to show or hide

When you realize the lil brother is dead, my jaw hit the fucking floor and i sat at pause for 2 mins like wtf just happend

Space Brothers(Fucking show chokes me up every episode never expected it to be so rich in story)